A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-07-08, 07:46 UTC
based on data in:
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, and DIA-NN.URL: https://github.com/bigbio/pmultiqc
Summary and HeatMap
Summary Table
This table shows the quantms pipeline summary statistics.
This table shows the quantms pipeline summary statistics.
Showing 1/1 rows.
| #Peptides Quantified | #Proteins Quantified |
|---|---|
| 3725 | 765 |
Pipeline Result Statistics
This plot shows the quantms pipeline final result.
Including Sample Name, Possible Study Variables, identified the number of peptide in the pipeline,
and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained
from the out_msstats file. You can also remove the decoy with the `remove_decoy` parameter.
Showing 12/12 rows and 4/4 columns.
| Sample Name | #Peptide IDs | #Unambiguous Peptide IDs | #Modified Peptide IDs | #Protein (group) IDs |
|---|---|---|---|---|
| 20221028_FL_Lu_SV_Set12_A1 | 2871 | 2871 | 402 | 793 |
| 20221028_FL_Lu_SV_Set12_A2 | 2877 | 2877 | 393 | 786 |
| 20221028_FL_Lu_SV_Set12_A3 | 2513 | 2513 | 336 | 688 |
| 20221028_FL_Lu_SV_Set12_A4 | 3001 | 3001 | 411 | 835 |
| 20221028_FL_Lu_SV_Set12_A5 | 2941 | 2941 | 413 | 818 |
| 20221028_FL_Lu_SV_Set12_A6 | 3020 | 3020 | 419 | 837 |
| 20221028_FL_Lu_SV_Set12_B1 | 2641 | 2641 | 350 | 759 |
| 20221028_FL_Lu_SV_Set12_B2 | 2766 | 2766 | 361 | 805 |
| 20221028_FL_Lu_SV_Set12_B3 | 3043 | 3043 | 408 | 888 |
| 20221028_FL_Lu_SV_Set12_B4 | 2887 | 2887 | 387 | 832 |
| 20221028_FL_Lu_SV_Set12_B5 | 2336 | 2336 | 313 | 669 |
| 20221028_FL_Lu_SV_Set12_B6 | 2517 | 2517 | 340 | 744 |
Identification Summary
Number of Peptides identified Per Protein
This plot shows the number of peptides per protein in quantms pipeline final result
This statistic is extracted from the out_msstats file. Proteins supported by more peptide
identifications can constitute more confident results.
ProteinGroups Count
Number of protein groups per raw file.
Based on statistics calculated from mzTab, mzIdentML (mzid), or DIA-NN report files.
Peptide ID Count
Number of unique (i.e. not counted twice) peptide sequences including modifications per Raw file.
Based on statistics calculated from mzTab, mzIdentML (mzid), or DIA-NN report files.
Modifications Per Raw File
Compute an occurence table of modifications (e.g. Oxidation (M)) for all peptides, including the unmodified.
Post-translational modifications contained within the identified peptide sequence.
MS1 Analysis
Total Ion Chromatograms
MS1 quality control information extracted from the spectrum files.
This plot displays Total Ion Chromatograms (TICs) derived from MS1 scans across all analyzed samples.
The x-axis represents retention time, and the y-axis shows the total ion intensity at each time point.
Each colored trace corresponds to a different sample. The TIC provides a global view of the ion signal
throughout the LC-MS/MS run, reflecting when compounds elute from the chromatography column.
Key aspects to assess include:
* Overall intensity pattern: A consistent baseline and similar peak profiles across samples indicate good reproducibility.
* Major peak alignment: Prominent peaks appearing at similar retention times suggest stable chromatographic performance.
* Signal-to-noise ratio: High peaks relative to baseline noise reflect better sensitivity.
* Chromatographic resolution: Sharp, well-separated peaks indicate effective separation.
* Signal drift: A gradual decline in signal intensity across the run may point to source contamination or chromatography issues.
Deviations such as shifted retention times, missing peaks, or inconsistent intensities may signal problems
in sample preparation, LC conditions, or mass spectrometer performance that require further investigation.
Created with MultiQC
MS1 Base Peak Chromatograms
MS1 base peak chromatograms extracted from the spectrum files.
The Base Peak Chromatogram (BPC) displays the intensity of the most abundant ion at each retention
time point across your LC-MS run. Unlike the Total Ion Chromatogram (TIC) which shows the summed
intensity of all ions, the BPC highlights the strongest signals, providing better visualization
of compounds with high abundance while reducing baseline noise. This makes it particularly useful
for identifying major components in complex samples, monitoring dominant species, and providing
clearer peak visualization when signal-to-noise ratio is a concern. Comparing BPC patterns across
samples allows you to evaluate consistency in the detection of high-abundance compounds
and can reveal significant variations in sample composition or instrument performance.
Created with MultiQC
MS1 Peaks
MS1 Peaks from the spectrum files
This plot shows the number of peaks detected in MS1 scans over the course of each sample run.
The x-axis represents retention time (in minutes), while the y-axis displays the number of
distinct ion signals (peaks) identified in each MS1 scan. The MS1 peak count reflects spectral
complexity and provides insight into instrument performance during the LC-MS analysis.
Key aspects to consider include:
* Overall pattern: Peak counts typically increase during the elution of complex mixtures and
decrease during column washing or re-equilibration phases.
* Peak density: Higher counts suggest more complex spectra, potentially indicating a greater
number of compounds present at that time point."
* Peak Consistency across samples: Similar profiles among replicates or related samples
indicate good analytical reproducibility.
* Sudden drops: Abrupt decreases in peak count may point to transient ionization issues,
spray instability, or chromatographic disruptions.
* Baseline values: The minimum peak count observed reflects the level of background noise
or instrument sensitivity in the absence of eluting compounds.
Monitoring MS1 peak counts complements total ion chromatogram (TIC) and base peak chromatogram
(BPC) data, offering an additional layer of quality control related to signal complexity,
instrument stability, and sample composition.
Created with MultiQC
General stats for MS1 information
General stats for MS1 information extracted from the spectrum files.
This table presents general statistics for MS1 information extracted from mass spectrometry data files."
It displays MS runs with their acquisition dates and times.
For each file, the table shows two key metrics: TotalCurrent (the sum of all MS1 ion intensities throughout the run) and ScanCurrent (the sum of MS2 ion intensities).
These values provide a quick overview of the total ion signals detected during both survey scans (MS1) and fragmentation scans (MS2),
allowing for comparison of overall signal intensity across samples. Consistent TotalCurrent and ScanCurrent values across similar samples typically
indicate good reproducibility in the mass spectrometry analysis, while significant variations may suggest issues with sample preparation,
instrument performance, or ionization efficiency. The blue shading helps visualize the relative intensity differences between samples.
Showing 12/12 rows and 3/3 columns.
| File | Acquisition Date Time | log10(Total Current) | log10(Scan Current) |
|---|---|---|---|
| 20221028_FL_Lu_SV_Set12_A1 | 2022-10-29 22:11:31 | 11.7957 | 11.3888 |
| 20221028_FL_Lu_SV_Set12_A2 | 2022-10-30 01:33:52 | 11.8052 | 34.2775 |
| 20221028_FL_Lu_SV_Set12_A3 | 2022-10-30 13:47:37 | 11.7305 | 11.3256 |
| 20221028_FL_Lu_SV_Set12_A4 | 2022-10-30 06:40:43 | 11.8220 | 11.4029 |
| 20221028_FL_Lu_SV_Set12_A5 | 2022-10-30 09:03:01 | 11.8009 | 11.3846 |
| 20221028_FL_Lu_SV_Set12_A6 | 2022-10-30 01:56:09 | 11.8099 | 11.4013 |
| 20221028_FL_Lu_SV_Set12_B1 | 2022-10-29 12:42:17 | 11.7506 | 11.3651 |
| 20221028_FL_Lu_SV_Set12_B2 | 2022-10-30 11:25:17 | 11.8033 | 11.3784 |
| 20221028_FL_Lu_SV_Set12_B3 | 2022-10-29 15:04:34 | 11.8335 | 11.4320 |
| 20221028_FL_Lu_SV_Set12_B4 | 2022-10-30 04:18:27 | 11.8097 | 11.4051 |
| 20221028_FL_Lu_SV_Set12_B5 | 2022-10-29 17:26:54 | 11.6971 | 11.3046 |
| 20221028_FL_Lu_SV_Set12_B6 | 2022-10-29 19:49:11 | 11.7172 | 11.3146 |
MS2 and Spectral Stats
Number of Peaks per MS/MS spectrum
This chart represents a histogram containing the number of peaks per MS/MS spectrum
in a given experiment.
This chart assumes centroid data. Too few peaks can identify poor fragmentation
or a detector fault, as opposed to a large number of peaks representing very noisy spectra.
This chart is extensively dependent on the pre-processing steps performed to the spectra
(centroiding, deconvolution, peak picking approach, etc).
Peak Intensity Distribution
This is a histogram representing the ion intensity vs.
the frequency for all MS2 spectra in a whole given experiment.
It is possible to filter the information for all, identified and unidentified spectra.
This plot can give a general estimation of the noise level of the spectra.
Generally, one should expect to have a high number of low intensity noise peaks with a low number
of high intensity signal peaks.
A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or
potential experimental problems. In the case of data reuse this plot can be useful in
identifying the requirement for pre-processing of the spectra prior to any downstream analysis.
The quality of the identifications is not linked to this data as most search engines perform internal
spectrum pre-processing before matching the spectra. Thus, the spectra reported are not
necessarily pre-processed since the search engine may have applied the pre-processing step
internally. This pre-processing is not necessarily reported in the experimental metadata.
Distribution of Precursor Charges
This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.
This information can be used to identify potential ionization problems
including many 1+ charges from an ESI ionization source or an unexpected
distribution of charges. MALDI experiments are expected to contain almost exclusively 1+
charged ions. An unexpected charge distribution may furthermore be caused by specific search
engine parameter settings such as limiting the search to specific ion charges.
